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Elucidation of the process of sex chromosome differentiation is necessary to understand the dynamics of evolutionary mechanisms in organisms. The W sex chromosome of the Siamese cobra (Naja kaouthia) contains a large number of repeats and shares amniote sex chromosomal linkages. Diversity Arrays Technology provides an effective approach to identify sex-specific loci that are epoch-making, to understand the dynamics of molecular transitions between the Z and W sex chromosomes in a snake lineage. From a total of 543 sex-specific loci, 90 showed partial homology with sex chromosomes of several amniotes and 89 loci were homologous to transposable elements. Two loci were confirmed as W-specific nucleotides after PCR amplification. These loci might result from a sex chromosome differentiation process and involve putative sex-determination regions in the Siamese cobra. Sex-specific loci shared linkage homologies among amniote sex chromosomes, supporting an ancestral super-sex chromosome. • 69 SNP loci and 474 PA loci was associated with sex-specific loci in females. • From a total of 543 sex-specific loci, 90 showed partial homology with sex chromosomes of several amniotes and 89 loci were homologous to transposable elements. • Two loci were confirmed as W-specific nucleotides after PCR amplification. These loci might result from a sex chromosome differentiation process and involve putative sex-determination regions in the Siamese cobra. • Sex-specific loci shared linkage homologies among amniote sex chromosomes, supporting an ancestral super-sex chromosome. [ABSTRACT FROM AUTHOR]

Telomeres comprise tandem repeated DNA sequences that protect the ends of chromosomes from deterioration or fusion with neighboring chromosomes, and their lengths might vary with sex and age. Here, age‐ and sex‐related telomere lengths in male and female captive Siamese cobras (Naja kaouthia) were investigated using quantitative real‐time polymerase chain reaction based on cross‐sectional data. A negative correlation was shown between telomere length and body size in males but not in females. Age‐related sex differences were also recorded. Juvenile female snakes have shorter telomeres relative to males at up to 5 years of age, while body size also rapidly increases during this period. This suggests that an accelerated increase in telomere length of female cobra results from sex hormone stimulation to telomerase activity, reflecting sexually dimorphic phenotypic traits. This might also result from amplification of telomeric repeats on sex chromosomes. By contrast, female Siamese cobras older than 5 years had longer telomeres than males. Diverse sex hormone levels and oxidative stress parameters between sexes may affect telomere length. [ABSTRACT FROM AUTHOR]

Taxonomic ranks above the species level are inherently arbitrary. However, there is a growing number of publications aimed at more consistent classifications with comparable ranks among taxa. For this study, we use a recently developed temporal approach that utilizes time-calibrated chronograms to identify and define temporal bands for comparable ordinal and family ranks in Lecanoromycetes, the most diverse lineage of lichen-forming fungi. A multi-locus dataset consisting of 539 taxa in the two major subclasses of Lecanoromycetes, Lecanoromycetidae and Ostropomycetidae, was used to address the circumscription of families and orders. Based on the temporal banding approach, clades that share a common ancestor between 176 and 194 Mya and a time window of 111–135 Mya correspond to order-level and family-level, respectively. Most currently accepted orders and families were supported in their current circumscription, but some new taxa are described. Here we propose a revised, temporally based classification for the two subclasses. Specifically, three new orders are proposed: Sporastatiales, Schaereriales and Thelenellales. Arctomiales, Hymeneliales and Trapeliales are synonymized with Baeomycetales. Varicellariaceae are proposed as a new family, and Diploschistaceae and Thelotremataceae are resurrected. Squamarinaceae and Stereocaulaceae are synonymized with Cladoniaceae, Carbonicolaceae are synonymized with Lecanoraceae, Letrouitiaceae are synonymized with Brigantiaeaceae, Lobariaceae and Nephromataceae are synonymized with Peltigeraceae, Thrombiaceae are synonymized with Protothelenellaceae, and Miltideaceae are synonymized with Agyriaceae. This study represents an important step towards more consistent, comparable deeper-level taxonomic rankings in the most diverse lineages of lichen-forming fungi. [ABSTRACT FROM AUTHOR]

Five new species of Graphidaceae are described from Thailand. Molecular evidence and phenotypical characters support their independent status from related and similar species. Glaucotrema thailandicum Naksuwankul, Lücking & Lumbsch is unique within the genus in having submuriform ascospores. Ocellularia klinhomii Naksuwankul, Lücking & Lumbsch is characterized by having a whitish gray, rimose thallus with ascomata in verrucae and surrounded by a black ring and lack of secondary metabolites. Ocellularia phatamensis Naksuwankul, Parnmen & Lumbsch has a grayish, thick and rimose thallus, differing from O. klinhomii in lacking a dark apothecial rim and having ascomata that are not immersed in verrucae. Ocellularia thailandica Naksuwankul, Kraichak & Lumbsch differs from O. albocincta in lacking a columella. Ocellularia rotundifumosa Naksuwankul, Lücking & Lumbsch differs from O. fumosa in having ascospores with rounded ends. An epitype for O. krathingensis is selected. [ABSTRACT FROM AUTHOR]

Identifying factors that influence species interactions is central to research in symbiotic systems. While lichens represent iconic models of symbiosis and play important roles in understanding the biology of symbiotic interactions, patterns of interactions in lichen symbionts and mechanisms governing these relationships are not well characterized. This is due, in part to the fact that current taxonomic approaches for recognizing diversity in lichen symbionts commonly fail to accurately reflect actual species diversity. In this study, we employed DNA-based approaches to circumscribed candidate species-level lineages in rock-posy lichen symbionts (mycobiont = Rhizoplaca s. lat. species; photobiont = Trebouxia species). Our results revealed a high degree of cryptic diversity in both the myco- and photobionts in these lichens. Using the candidate species circumscribed here, we investigated the specificity of the symbionts toward their partners and inferred the relative importance of various factors influencing symbiont interactions. Distinct mycobiont species complexes, ecozones, and biomes are significantly correlated with the occurrence of photobiont OTUs, indicating that complex interactions among mycobiont lineages, ecogeography, and microhabitat determine interactions between photobionts and their mycobionts in lichen symbiosis. One-to-one specificity between mycobiont and photobiont species was not found, with the exception of R. maheui that associated with a single Trebouxia OTU that was not found with other Rhizoplaca s. lat. species. We estimated the most recent common ancestor of the core Rhizoplaca group at c. 62.5 Ma, similar in age to the diverse parmelioid core group in the well-studied family Parmeliaceae. However, in contrast to Parmeliaceae, species in Rhizoplaca were found to associate with a narrow range of photobionts. Our study provides important perspectives into species diversity and interactions in iconic lichen symbiotic systems and establishes a valuable framework for continuing research into rock-posy lichens. [ABSTRACT FROM AUTHOR]

Premise of research. With more than 2000 described species, Graphidaceae represents one of the largest families of lichenized fungi. The underlying causes for such a high level of diversity have not yet been studied in detail. Two possible drivers of high diversity in this group include its predominantly tropical habitat, a major factor for high species richness in other groups of organisms, and the presence of columella, a unique trait within this family. Methodology. We employed a combination of comparative methods to investigate possible factors that are associated with the hyperdiverse nature of the family, including modeling evolutionary diversity using stepwise Akaike information criterion (MEDUSA) to identify clades with an increased diversification rate and binary state speciation and extinction (BiSSE) analysis to determine whether diversification rates change in association with selected character states. Pivotal results. BiSSE analysis revealed a significantly higher diversification rate in the lineages with presence of a columella, while there was no significant difference in diversification rates between tropical and nontropical lineages. A further analysis with MEDUSA also identified two or three diversification rate shifts, one of which occurred in the Ocellularia clade, with a large number of species with a columella. Conclusions. The results suggest a stronger role of the columella, compared to tropical habitat, in driving high levels of diversification in the family. The possible ecomorphological importance of columella structures is discussed. [ABSTRACT FROM AUTHOR]

One new species and six new records of the crustose lichenized genus Graphis are reported from Thailand. Graphis koratensis Pitakpong, Kraichak & Lücking sp. nov. is characterized by lirelline ascocarps with whitish grey or grey-green pruina along the slit, transversely septate ascospores, and the presence of norstictic acid. Phylogenetic analyses with two loci (mtSSU and nuLSU) show the distinct position of this new species within the genus. Six new records for Thailand are reported, including G. cincta (Pers.) Aptroot, G. jejuensis K. H. Moon et al., G. nigrocarpa Adaw. & Makhija, G. renschiana (Müll. Arg.) Stizenb., G. seminuda Müll. Arg., and G. subserpentina Nyl. [ABSTRACT FROM AUTHOR]

Graphis scripta, or script lichen, is a well-known species of crustose lichenized fungi, widely distributed in the temperate region of the Northern Hemisphere. It is now considered to be a species complex, but because of the lack of secondary chemistry and paucity of measurable morphological characters, species delimitation within the complex has been challenging and is thus far based on apothecium and ascospore morphology. In this study, we employed molecular as well as morphological data to assess phylogenetic structure and delimitation of lineages within the G. scripta complex. We generated sequences for four genetic markers (mtSSU, nuLSU, RPB2, and EF-1) and performed phylogenetic analyses. The resulting trees were used to determine the number of distinct lineages by applying a general mixed Yule-coalescent (GMYC) model and species tree estimation through maximum likelihood (STEM). Our analyses suggest between six and seven putative species within the G. scripta complex. However, these did not correspond to the taxa that were recently distinguished based on apothecium morphology and could not be circumscribed with the morphological characters that were traditionally used in the classification of the complex. Any formal taxonomic treatment will require additional sampling and evaluation of additional traits that potentially can characterize these clades. [ABSTRACT FROM AUTHOR]

Microbial symbionts are instrumental to the ecological and long-term evolutionary success of their hosts, and the central role of symbiotic interactions is increasingly recognized across the vast majority of life. Lichens provide an iconic group for investigating patterns in species interactions; however, relationships among lichen symbionts are often masked by uncertain species boundaries or an inability to reliably identify symbionts. The species-rich lichen-forming fungal family Parmeliaceae provides a diverse group for assessing patterns of interactions of algal symbionts, and our study addresses patterns of lichen symbiont interactions at the largest geographic and taxonomic scales attempted to date. We analysed a total of 2356 algal internal transcribed spacer ( ITS) region sequences collected from lichens representing ten mycobiont genera in Parmeliaceae, two genera in Lecanoraceae and 26 cultured Trebouxia strains. Algal ITS sequences were grouped into operational taxonomic units ( OTUs); we attempted to validate the evolutionary independence of a subset of the inferred OTUs using chloroplast and mitochondrial loci. We explored the patterns of symbiont interactions in these lichens based on ecogeographic distributions and mycobiont taxonomy. We found high levels of undescribed diversity in Trebouxia, broad distributions across distinct ecoregions for many photobiont OTUs and varying levels of mycobiont selectivity and specificity towards the photobiont. Based on these results, we conclude that fungal specificity and selectivity for algal partners play a major role in determining lichen partnerships, potentially superseding ecology, at least at the ecogeographic scale investigated here. To facilitate effective communication and consistency across future studies, we propose a provisional naming system for Trebouxia photobionts and provide representative sequences for each OTU circumscribed in this study. [ABSTRACT FROM AUTHOR]

The phylogenetic placement of Chapsa lamellifera, C. megalophthalma and Diploschistes ocellatus was studied using a dataset of five genetic markers (mtSSU, nuLSU, RPB1, RPB2 and ITS). As extratropical species occurring in Australasia, C. lamellifera and C. megalophthalma differ from other species in that genus by having relatively large ascomata with muriform ascospores and complex chemistry of either the protocetraric or stictic acids chemosyndrome. D. ocellatus is unique within Diploschistes, in lacking lateral paraphyses and containing the norstictic acid chemosyndrome. Previous phylogenetic analysis gave inconclusive results regarding the phylogenetic position of these taxa, and hence in the present study, a larger sampling of molecular markers was employed. Our results demonstrated that the two Chapsa species and D. ocellatus are not part of their current genera. Consequently, the new genera Gintarasia Kraichak, Lücking & Lumbsch and Xalocoa Kraichak, Lücking & Lumbsch are described to accommodate these species. The new combinations Gintarasia lamellifera (Kantvilas & Vézda) Kraichak, Lücking & Lumbsch, G lordhowensis (Mangold) Kraichak, Lücking & Lumbsch, G megalophthalma (Müll. Arg.) Kraichak, Lücking & Lumbsch and Xalocoa ocellata (Vill.) Kraichak, Lücking & Lumbsch are also proposed. [ABSTRACT FROM AUTHOR]

* Premise of the study: Many links between form and function are described in the context of adaptation. Several morphological and life-history traits in the leafy liverwort family Lejeuneaceae (Marchantiophyta) have been hypothesized to be adaptations for living on the surface of leaves of vascular plants (epiphylly). There have been, however, no rigorous tests of these hypotheses. * Methods: Using a recently published phylogeny of Lejeuneaceae and trait data from published monographs, I tested the correlations of putative adaptive traits with the incidence of epiphylly. Both cross-species and phylogenetic-based analyses of trait data were performed to distinguish the patterns of shared evolutionary history from independent origins of putatively adaptive traits. The rates of transitions between different combinations of character states were also calculated to determine whether traits were more likely to evolve in the presence of epiphylly. * Key results: Only one trait, production of asexual propagules, was correlated with epiphylly in the phylogenetic-based analysis. The rate of transition to asexual propagules was also significantly higher in the presence of epiphylly. Other traits correlated with epiphylly appeared to be the results of shared evolutionary history among sister taxa and therefore not due to adaptive evolution. * Conclusion: The present study distinguished production of asexual propagules from other traits as a key adaptive response to living on the leaf surface. No other putative "adaptive" traits to epiphylly showed evidence of being specific adaptation to epiphylly. The results highlight the importance of phylogenetically controlled methods in determining an adaptive function of traits. [ABSTRACT FROM AUTHOR]

The North African catfish (Clarias gariepinus) is a significant species in aquaculture, which is crucial for ensuring food and nutrition security. Their high adaptability to diverse environments has led to an increase in the number of farms that are available for their production. However, long-term closed breeding adversely affects their reproductive performance, leading to a decrease in production efficiency. This is possibly caused by inbreeding depression. To investigate the root cause of this issue, the genetic diversity of captive North African catfish populations was assessed in this study. Microsatellite genotyping and mitochondrial DNA D-loop sequencing were applied to 136 catfish specimens, collected from three populations captured for breeding in Thailand. Interestingly, extremely low inbreeding coefficients were obtained within each population, and distinct genetic diversity was observed among the three populations, indicating that their genetic origins are markedly different. This suggests that outbreeding depression by genetic admixture among currently captured populations of different origins may account for the low productivity of the North African catfish in Thailand. Genetic improvement of the North African catfish populations is required by introducing new populations whose origins are clearly known. This strategy should be systematically integrated into breeding programs to establish an ideal founder stock for selective breeding. [ABSTRACT FROM AUTHOR]

Leucobryum aduncum is a moss species reported in many Southeast Asian regions, often found in forests with a high humidity. Climate change may impact the future distribution of this species. This study aimed to model the current distribution and predict the impact of climate change on L. aduncum distribution in the next 50 years across Southeast Asia. In the process, relevant climate variables in the distribution of the species were also identified. The occurrence data of this species with current and future climate models from CMIP6 under moderate (SSP2) scenarios were used to predict current and future L. aduncum distributions. Under the current climate, the predicted suitable areas for L. aduncum included most mountainous areas. However, many Southeast Asian areas showed a lower probability of finding this species in the next 50 years. The distribution area of this species will dramatically decrease by 50.16% in the current area. The most important ecological variables included the "mean temperature of the driest quarter" and the "annual temperature range". This study suggests the possible impacts of an increased temperature and the scale of climate change on the distribution of sensitive plants like bryophytes. [ABSTRACT FROM AUTHOR]

Historical mass extinction events had major impacts on biodiversity patterns. The most recent and intensively studied event is the Cretaceous – Paleogene (K-Pg) boundary (ca. 66 million years ago [MYA]). However, the factors that may have impacted diversification dynamics vary across lineages. We investigated the macroevolutionary dynamics with a specific focus on the impact of major historical events such as the K-Pg mass extinction event on two major subclasses – Lecanoromycetidae and Ostropomycetidae – of lichen-forming fungi and tested whether variation in the rate of diversification can be associated with the evolution of a specific trait state - macrolichen. Our results reveal accelerated diversification events in three families of morphologically complex lichen-forming fungi – Cladoniaceae, Parmeliaceae, and Peltigeraceae – which are from the subclass Lecanoromycetidae and mostly composed of macrolichens, those that form three dimensional structures. Our RTT plot result for the subclass Lecanoromycetidae also reveals accelerated diversification. Changes in diversification rates occurred around the transition between Mesozoic and Cenozoic eras and was likely related to the K-Pg mass extinction event. The phylogenetic positions for rate increases estimated based on marginal shift probability are, however, scattered from 100 to 40 MYA preventing us from making explicit inference. Although we reveal that the phenotypic state of macrolichens is associated with a higher diversification rate than microlichens, we also show that the evolution of macrolichens predated the K-Pg event. Furthermore, the association between macrolichens and increased diversification is not universal and can be explained, in part, by phylogenetic relatedness. By investigating the macroevolutionary dynamics of lichen-forming fungi our study provides a new empirical system suitable to test the effect of major historical event on shaping biodiversity patterns and to investigate why changes in biodiversity patterns are not in concordance across clades. Our results imply that multiple historical events during the transition from Mesozoic to Cenozoic eras, including the K-Pg mass extinction event, impacted the evolutionary dynamics in lichen-forming fungi. However, future studies focusing on individual lichen-forming fungal families are required to ascertain whether diversification rates are associated with growth form and certain geological events. [ABSTRACT FROM AUTHOR]

Simple Summary: Hybrids between the critically endangered Siamese crocodile (Crocodylus siamensis) and least-concern saltwater crocodile (C. porosus) pose a significant challenge to conservation efforts due to human activities. Previous studies used microsatellite and mitochondrial DNA data to identify these hybrids, but potential biases and genetic drift within the populations could influence the results. To address these limitations and gain a clearer understanding of the genetic dynamics, we employed DArT sequencing to identify genome-wide single nucleotide polymorphisms (SNPs) in both species and confirm hybrid scenarios. We compared a population of Australian saltwater crocodiles to assess species-specific SNP distribution. Various analytical approaches were used to diagnose hybridization levels, especially in cases with potential backcrossing. Approximately 17.00–26.00% of loci were shared between Siamese and saltwater crocodile genomes. We identified 8051 species-specific SNP loci for Siamese crocodiles and 1288 for saltwater crocodiles. Using a PCR-based approach, three SNP loci were developed as markers, successfully enabling the distinction between species and various levels of hybridization. By combining mitochondrial and nuclear genetic information with species-diagnostic DNA markers, we developed a novel method for conservation prioritization, aiding long-term species survival through reintroduction and management programs. Hybrids between the critically endangered Siamese crocodile (Crocodylus siamensis) and least-concern saltwater crocodile (C. porosus) in captive populations represent a serious challenge for conservation and reintroduction programs due to the impact of anthropogenic activities. A previous study used microsatellite and mitochondrial DNA data to establish the criteria for identifying species and their hybrids; however, the results may have been influenced by biased allelic frequencies and genetic drift within the examined population. To overcome these limitations and identify the true signals of selection, alternative DNA markers and a diverse set of populations should be employed. Therefore, this study used DArT sequencing to identify genome-wide single nucleotide polymorphisms (SNPs) in both species and confirm the genetic scenario of the parental species and their hybrids. A population of saltwater crocodiles from Australia was used to compare the distribution of species-diagnostic SNPs. Different analytical approaches were compared to diagnose the level of hybridization when an admixture was present, wherein three individuals had potential backcrossing. Approximately 17.00–26.00% of loci were conserved between the Siamese and saltwater crocodile genomes. Species-diagnostic SNP loci for Siamese and saltwater crocodiles were identified as 8051 loci and 1288 loci, respectively. To validate the species-diagnostic SNP loci, a PCR-based approach was used by selecting 20 SNP loci for PCR primer design, among which 3 loci were successfully able to differentiate the actual species and different hybridization levels. Mitochondrial and nuclear genetic information, including microsatellite genotyping and species-diagnostic DNA markers, were combined as a novel method that can compensate for the limitations of each method. This method enables conservation prioritization before release into the wild, thereby ensuring sustainable genetic integrity for long-term species survival through reintroduction and management programs. [ABSTRACT FROM AUTHOR]

This study addressed the environmental factors that affect Trentepohlia spp. in the Chiang Dao Wildlife Sanctuary at altitudes of 399 to 1,503 meters above sea level (m a.s.l.) during the rainy, winter, and summer seasons. Species were identified using characteristic morphological identification. Te influence of environmental factors on the algae was analyzed using a statistical program, and seasonal changes in the quantity of photosynthetic pigments in the dominant species were evaluated. Te average relative humidity was 69.34 ± 12.90%, the average temperature was 26.23 ± 3.79 °C, and the average light intensity was 139.78 ± 42.21 µmol photon m-2 s-1. Thirteen species were found: Trentepohlia chapmanii, Trentepohlia sp. 1, Trentepohlia sp. 2, Trentepohlia sundarbanensis, Trentepohlia sp. 3, Trentepohlia rigidula, Trentepohlia sp. 4, Trentepohlia efusa, Trentepohlia monilia, Trentepohlia abietina, Trentepohlia sp. 5, Trentepohlia aurea, and Trentepohlia umbrina. Te largest number of species (seven to nine) were found at lower altitudes, from 473 to 517 m a.s.l. Species diversity was greatest in the winter season (13 species). Species found at low attitude were grouped together (Group 1) and had the greatest diversity, and the remaining species were divided into Groups 2, 3, and 4. Environmental factors had both positive and negative influences on the species, especially T. chapmanii, which was found below 1,003 m a.s.l., and T. monilia, which was found in areas with a high relative humidity of 74.50% to 83.93%. Te ratio of the total carotenoids to chlorophyll of T. rigidula, the dominant species, was relatively high at 4.96:1, and the β-carotene content (46.89 %w/w) was highest during winter. [ABSTRACT FROM AUTHOR]

Simple Summary: Microsatellite markers are widely used molecular markers for genetic studies, but choosing the right set involves a challenging trade-off between effectiveness and cost. The research aims to enhance the widely used ant colony optimization algorithm by integrating marker effectiveness indicators. By considering the genetic properties of the markers such as the polymorphic information content, the study seeks to determine the suitable way to select a reduced set of microsatellites. The approach addresses the accuracy–cost trade-off, aiding genetic assessments, breeding, and conservation efforts with cost-effective solutions. This research provides valuable insights into real-world genetic studies, including breeding programs and conservation initiatives. Microsatellites are polymorphic and cost-effective. Optimizing reduced microsatellite panels using heuristic algorithms eases budget constraints in genetic diversity and population genetic assessments. Microsatellite marker efficiency is strongly associated with its polymorphism and is quantified as the polymorphic information content (PIC). Nevertheless, marker selection cannot rely solely on PIC. In this study, the ant colony optimization (ACO) algorithm, a widely recognized optimization method, was adopted to create an enhanced selection scheme for refining microsatellite marker panels, called the PIC–ACO selection scheme. The algorithm was fine-tuned and validated using extensive datasets of chicken (Gallus gallus) and Chinese gorals (Naemorhedus griseus) from our previous studies. In contrast to basic optimization algorithms that stochastically initialize potential outputs, our selection algorithm utilizes the PIC values of markers to prime the ACO process. This increases the global solution discovery speed while reducing the likelihood of becoming trapped in local solutions. This process facilitated the acquisition of a cost-efficient and optimized microsatellite marker panel for studying genetic diversity and population genetic datasets. The established microsatellite efficiency metrics such as PIC, allele richness, and heterozygosity were correlated with the actual effectiveness of the microsatellite marker panel. This approach could substantially reduce budgetary barriers to population genetic assessments, breeding, and conservation programs. [ABSTRACT FROM AUTHOR]

Species of lichen-forming fungi (LFF) display an array of geographical distribution patterns. Among the broadly distributed lichen-forming fungal species, the degree of reproductive isolation and genetic substructure among populations varies widely, in some cases masking unrecognized diversity or meaningful biogeographical patterns. Lecidea atrobrunnea (Raymond ex Lam. & DC.) Schaer. s. lat. (Lecideaceae) is a widespread species complex that has been studied for over two centuries since its initial description. The diversity of the L. atrobrunnea group is highest in western North America, where a dizzying array of morphologies and chemistry can occur at local scales. Here we investigate whether the assumed cosmopolitan distribution of L. atrobrunnea s. lat. is an artifact of taxonomic limitations and masks biogeographical patterns in this species complex. To address these questions, we compiled sequence data from the standard fungal barcoding marker (ITS) for over 100 specimens within this complex, in addition to genome-scale data from a subset of these representing over 1600 single-copy nuclear genes spanning over 3 Mb of the genome. Our study corroborates the perspective that the morphologically and chemically variable Lecidea atrobrunnea group reflects a complex of distinct species-level lineages, with 42–83 candidate species inferred from the ITS region and high levels of diversity inferred from a subset of specimens using genome-scale data. However, both phenotype- and molecular-based species boundaries remained unsettled, with the most common nominal taxa recovered as highly polyphyletic and with conflict among different molecular species delimitation approaches. Our study also highlights the potential for geographically restricted species, with fascinating biogeographical patterns, challenging, in part, the assumed cosmopolitan distribution of L. atrobrunnea s. lat. This study provides valuable direction for future research that will be crucial in understanding diversification and establishing a robust taxonomy for this well-known species complex. [ABSTRACT FROM AUTHOR]

Cassava breeding is a critical aspect of sustainable agriculture to address the challenges of food security and climate change. The present study aimed to assess the combining ability of six Thai cassava elite varieties for four key traits, including fresh root yield (FRY), fresh shoot yield (FSY), harvest index (HI) and starch content (SC) through an analysis of the diallel mating design over two years. Parental lines HB80 and R5 showed significant positive general combining ability (GCA) effects for high SC; R1 and HB80 for low FSY; and R1 for high FRY and HI. The genetic effects for FSY, SC and HI were primarily influenced by the GCA of the progenitors, while specific combining ability (SCA) was more important for the FRY than the other three traits. Cultivation conditions were also found to impact the evaluation of genetic effects, with a poor growing environment affecting the expression of the genotype. This study provides a useful basis for the selection of parental lines for cassava breeding programs and insights into the genetic control of yield and related traits in the Thai elite cassava germplasm. [ABSTRACT FROM AUTHOR]

Leucobryum scalare was described in 1904 but its taxonomic status has been disputed, being reduced to a variety of Leucobryum aduncum or synonymized with Leucobryum aduncum. The taxonomic confusion of this taxon has remained unresolved. Hence, we revisited the taxonomic status of the taxon using phylogenetic and morphometric approaches. A total of 27 samples from Leucobryum aduncum var. aduncum and Leucobryum aduncum var. scalare were used to generate data from four markers, including ITS1, ITS2, atpB-rbcL spacer, and trnL-trnF. The concatenated dataset was used to reconstruct a phylogenetic tree. Both qualitative and quantitative morphological characters were measured and analyzed with Principal Component Analysis (PCA) and PERMANOVA. The results showed that the two taxa are closely related but they are reciprocally monophyletic. Both qualitative and quantitative characters could also separate Leucobryum aduncum var. scalare from Leucobryum aduncum var. aduncum as shown with PCA and PERMANOVA. We propose the resurrection of the species rank for Leucobryum scalare as separate from Leucobryum aduncum. This work highlights the need for a more thorough revision of Leucobryum to clarify the actual level of diversity in this genus. [ABSTRACT FROM AUTHOR]

Hybrid sterility, a hallmark of postzygotic isolation, arises from parental genome divergence disrupting meiosis. While chromosomal incompatibility is often implicated, the underlying mechanisms remain unclear. This study investigated meiotic behavior and genome-wide divergence in bighead catfish (C. macrocephalus), North African catfish (C. gariepinus), and their sterile male hybrids (important in aquaculture). Repetitive DNA analysis using bioinformatics and cytogenetics revealed significant divergence in satellite DNA (satDNA) families between parental species. Notably, one hybrid exhibited successful meiosis and spermatozoa production, suggesting potential variation in sterility expression. Our findings suggest that genome-wide satDNA divergence, rather than chromosome number differences, likely contributes to meiotic failure and male sterility in these catfish hybrids. • This study identifies meiotic failure as the primary cause of sterility in bighead catfish-North African catfish hybrids. • Chromosomal incompatibility likely causes hybrid sterility due to partial or complete absence of homologous chromosome synapsis. • Divergence in satellite DNA, like bighead catfish satDNA in a North African catfish, suggests repetitive DNA's role in reproductive isolation. • Interspecific satDNA transfer indicates possible limited genetic exchange events between these catfish species. [ABSTRACT FROM AUTHOR]

Centromeric satellite DNA (cen-satDNA) consists of highly divergent repeat monomers, each approximately 171 base pairs in length. Here, we investigated the genetic diversity in the centromeric region of two primate species: long-tailed (Macaca fascicularis) and rhesus (Macaca mulatta) macaques. Fluorescence in situ hybridization and bioinformatic analysis showed the chromosome-specific organization and dynamic nature of cen-satDNAsequences, and their substantial diversity, with distinct subfamilies across macaque populations, suggesting increased turnovers. Comparative genomics identified high level polymorphisms spanning a 120 bp deletion region and a remarkable interspecific variability in cen-satDNA size and structure. Population structure analysis detected admixture patterns within populations, indicating their high divergence and rapid evolution. However, differences in cen-satDNA profiles appear to not be involved in hybrid incompatibility between the two species. Our study provides a genomic landscape of centromeric repeats in wild macaques and opens new avenues for exploring their impact on the adaptive evolution and speciation of primates. [ABSTRACT FROM AUTHOR]

Fishes provide a unique and intriguing model system for studying the genomic origin and evolutionary mechanisms underlying sex determination and high sex-chromosome turnover. In this study, the mode of sex determination was investigated in Siamese fighting fish, a species of commercial importance. Genome-wide SNP analyses were performed on 75 individuals (40 males and 35 females) across commercial populations to determine candidate sex-specific/sex-linked loci. In total, 73 male-specific loci were identified and mapped to a 5.6 kb region on chromosome 9, suggesting a putative male-determining region (pMDR) containing localized dmrt1 and znrf3 functional sex developmental genes. Repeat annotations of the pMDR revealed an abundance of transposable elements, particularly Ty3/Gypsy and novel repeats. Remarkably, two out of the 73 male-specific loci were located on chromosomes 7 and 19, implying the existence of polygenic sex determination. Besides male-specific loci, five female-specific loci on chromosome 9 were also observed in certain populations, indicating the possibility of a female-determining region and the polygenic nature of sex determination. An alternative explanation is that male-specific loci derived from other chromosomes or female-specific loci in Siamese fighting fish recently emerged as new sex-determining loci during domestication and repeated hybridization. [ABSTRACT FROM AUTHOR]

Graphidaceae is a large family of over 2000 predominantly tropical, lichenized fungal species encompassing a remarkable range of morphological and chemical diversity. The majority of species belongs in subfamily Graphidoideae, which also exhibits the greatest amount of variation. Various phenotype characters have traditionally been used for classification at the genus and species levels, but their correlations with phylogenetic clades are poorly known. Using a multilocus approach, we reconstructed a phylogeny for 224 taxa, representing all main genera within subfamily Graphidoideae, and employed ancestral character reconstruction and character transformation analyses to understand the evolution of morphological, anatomical and chemical characters within this group. In addition, we examined the changes of habitat and photobiont types over the phylogeny. For this purpose, we focused on 10 characters, including thallus and ascoma features and chemistry. Since previous studies have shown that results may differ depending on the reconstruction method used, both Maximum-parsimony and Maximum-likelihood approaches were employed and multistate coding of characters was used. We reconstructed the ancestral states for 64 well-supported major clades in the family and found support for the ancestor of Graphidoideae being a tropical species with a trentepohlioid photobiont, apothecioid, solitary ascomata lacking both a columella and lateral paraphyses, and having non-amyloid ascospores. The frequency of transformations of morphological and chemical characters over the phylogeny of Graphidaceae was computed, resulting in a high frequency of reversible transformations for some characters, such as secondary chemistry, whereas other characters, such as photobiont, hymenial persistence or ascoma aggregation, exhibited low frequency of transformations. However, we found that even in the character with the highest number of transformations, secondary chemistry, the shifts were highly structured phylogenetically, suggesting that the evolution of the character, rather than the character state itself, can be used to predict phylogenetic relationships with certain accuracy. [ABSTRACT FROM PUBLISHER]

The snakeskin gourami (Trichopodus pectoralis) has a high meat yield and is one of the top five aquaculture freshwater fishes in Thailand. The species is not externally sexually dimorphic, and its sex determination system is unknown. Understanding the sex determination system of this species will contribute to its full-scale commercialization. In this study, a cytogenetic analysis did not reveal any between-sex differences in chromosomal patterns. However, we used genotyping-by-sequencing to identify 4 male-linked loci and 1 female-linked locus, indicating that the snakeskin gourami tends to exhibit an XX/XY sex determination system. However, we did not find any male-specific loci after filtering the loci for a ratio of 100:0 ratio of males:females. This suggests that the putative Y chromosome is young and that the sex determination region is cryptic. This approach provides solid information that can help identify the sex determination mechanism and potential sex determination regions in the snakeskin gourami, allowing further investigation of genetic improvements in the species. [ABSTRACT FROM AUTHOR]

Koponobryum papillosum Printarakul & Chantanaorr., sp. nov., is described as a second species of the genus found in Chiang Mai and Lamphun Provinces, northern Thailand. It is distinguished from K. bengalense (Gangulee) Arts by autoicous plants, papillose spores and axillary hairs consisting of one short basal cell and 1-4(5) longer upper cells. A taxonomic description, illustrations and SEM micrographs are presented. [ABSTRACT FROM AUTHOR]

Centromeric satellite DNA (cen-satDNA) sequences of the Asian swamp eel (Monopterus albus) were characterized. Three GC-rich cen-satDNA sequences were detected as a 233 bp MALREP-A and a 293 bp MALREP-B localized to all chromosomes, and a 293 bp MALREP-C distributed on eight chromosome pairs. Sequence lengths of MALREP-B and MALREP-C were 60 bp larger than that of MALREP-A, showing partial homology with core sequences (233 bp). Size differences between MALREP-A and MALREP-B/C suggest the possible occurrence of two satDNA families. The presence of an additional 60 bp in MALREP-B/C resulted from an ancient dimer of 233 bp monomers and subsequent mutation and homogenization between the two monomers. All MALREPs showed partial homology with transposable elements (TEs), suggesting that the MALREPs originated from the TEs. The MALREPs might have been acquired in the Asian swamp eel, thereby promoting fixation in the species. • Three centromeric satellite DNA sequences were isolated from the Asian swamp eel. • All MALREPs originated from the transposable elements. [ABSTRACT FROM AUTHOR]

The fragmentation of habitats and hunting have impacted the Asian woolly-necked stork (Ciconia episcopus), leading to a serious risk of extinction in Thailand. Programs of active captive breeding, together with careful genetic monitoring, can play an important role in facilitating the creation of source populations with genetic variability to aid the recovery of endangered species. Here, the genetic diversity and population structure of 86 Asian woolly-necked storks from three captive breeding programs [Khao Kheow Open Zoo (KKOZ) comprising 68 individuals, Nakhon Ratchasima Zoo (NRZ) comprising 16 individuals, and Dusit Zoo (DSZ) comprising 2 individuals] were analyzed using 13 microsatellite loci, to aid effective conservation management. Inbreeding and an extremely low effective population size (Ne) were found in the KKOZ population, suggesting that deleterious genetic issues had resulted from multiple generations held in captivity. By contrast, a recent demographic bottleneck was observed in the population at NRZ, where the ratio of Ne to abundance (N) was greater than 1. Clustering analysis also showed that one subdivision of the KKOZ population shared allelic variability with the NRZ population. This suggests that genetic drift, with a possible recent and mixed origin, occurred in the initial NRZ population, indicating historical transfer between captivities. These captive stork populations require improved genetic variability and a greater population size, which could be achieved by choosing low-related individuals for future transfers to increase the adaptive potential of reintroduced populations. Forward-in-time simulations such as those described herein constitute the first step in establishing an appropriate source population using a scientifically managed perspective for an in situ and ex situ conservation program in Thailand. [ABSTRACT FROM AUTHOR]

Premise of the Study: Studies on the diversity of epiphyllous bryophytes have been limited because of minute and incomplete specimens and a lack of taxonomic expertise. The recent development of the DNA barcoding approach has allowed taxon identification and species discovery of many obscure groups of organisms. Methods: With DNA extractions from 99 samples of 16 species, we compared the efficiencies of six DNA markers (rbcL, matK, trnL‐F, psbA, ITS1, and ITS2) in their ability to amplify, using a standard set of primers, as well as their discriminatory power, using distance‐based and tree‐based approaches with nucleotide data. Results: The amplification success was relatively high (70–90%) with all of the markers, except for matK, which yielded no success. The barcoding gap, as calculated from the difference between inter‐ and intraspecific genetic distances, was the highest in ITS2, whereas the highest numbers of monophyletic groups were found with ITS2 and rbcL. Discussion: rbcL should be used as a main barcoding marker with the addition of ITS2 for epiphyllous species. The development of DNA barcoding as a tool for quantifying species diversity will provide a rapid and reliable identification tool for epiphyllous bryophytes. [ABSTRACT FROM AUTHOR]

A new revised checklist of lichenized fungi in Thailand is presented, including 1,292 species. Recent work on the taxonomy of these organisms in Thailand resulted in an enormous increase in our knowledge of the lichen biota of the country - the current checklist includes more than twice as many species as the previous catalogue published 15 years ago - and phylogenetic studies resulted in numerous changes in the generic classification of lichenized fungi. Hence, a new checklist is here presented summarizing the current knowledge of lichens in Thailand. Six new records are reported, viz. Acanthothecis salazinica, Bactrospora metabola, Buellia parastata, Diploschistes cinereocaesius, Rolfidium coccocarpioides, and Trapelia placodioides. Five previously recorded species, namely Lecanora carpinea, Platismatia glauca, P. lacunosa, P. tuckermanii and Roccella phycopsis are shown to be based on misidentifications and are excluded from the checklist. Three new combinations of species previously placed in Pertusaria to Lepra are proposed: L. bulolensis (A.W.Archer, Elix & Streimann) Schmitt & Lumbsch, L. patellifera (A.W.Archer) Schmitt & Lumbsch, and L. subventosa (Malme) Schmitt & Lumbsch. [ABSTRACT FROM AUTHOR]

Accurate species delimitation is important as species are a fundamental unit in ecological, evolutionary and conservation biology research. In lichenized fungi, species delimitation has been difficult due to a lack of taxonomically important characteristics and due to the limits of traditional, morphology-based species concepts. In this study we reassess the current taxonomy of the Parmotrema perforatum group, which recognizes six closely related species divided into three species pairs, each pair comprising one apotheciate (sexual) and one sorediate (asexual) species. Each pair is further characterized by a distinct combination of secondary metabolites. It was hypothesized that the three apotheciate species are reproductively isolated sibling species and that each sorediate species evolved once from the chemically identical apotheciate species. In this study, species boundaries were re-examined using an integrative approach incorporating morphological, chemical and molecular sequence data to delimit species boundaries. Phylogenetic trees were inferred from a seven-locus DNA sequence dataset using concatenated gene tree and coalescent-based species-tree inference methods. Furthermore, we employed a multi-species coalescent method to validate candidate species. Micromorphological measurements of conidia were found to be congruent with phylogenetic clusters. Each approach that we applied to the P. perforatum group consistently recovered four of the currently circumscribed species ( P. perforatum, P. hypotropum, P. subrigidum and P. louisianae), whereas P. preperforatum and P. hypoleucinum were consistently combined and are thus interpreted as conspecific. [ABSTRACT FROM AUTHOR]

Molecular phylogenetic analysis presents two challenges when it is transformed into formal classifications: the taxonomic challenge (whether and how to distinguish monophyletic sister clades or how to deal with paraphyletic grades) and the nomenclatural challenge (naming clades, i.e. placing name-giving types accurately on a tree). One approach to the latter is morphology-based phylogenetic binning, which places specimens based on phenotypic features on a molecular tree and assigns uncertainty values to alternative placement options. Here, we use the example of the lichenized fungal genus L eptotrema to demonstrate how morphology-based phylogenetic binning can help to clarify taxonomic and nomenclatural issues when naming phylogenetically defined entities. L eptotrema is known for a common and widespread species, L . wightii, and phylogenetic analyses have been based exclusively on this species, including the recognition of a separate tribe, Leptotremateae. However, the genus name L eptotrema and the tribal name Leptotremateae are based on the name L . zollingeri, which was initially considered to be a synonym of L . wightii, but has recently been shown to represent a distinct species. As L . zollingeri differs considerably in phenotypic features from L . wightii, it can be questioned whether the two are at all related or whether L . zollingeri is actually closer to the genera M yriotrema and O cellularia in tribe Ocellularieae. The solution to this problem is not trivial, as it affects the correct use of the names Leptotrema and Leptotremateae. Morphology-based phylogenetic binning indeed demonstrated that L . zollingeri clusters with the M yriotrema album group in tribe Ocellularieae with high support. Hence, in contrast with current use, the name L eptotrema becomes available for the M . album group and Leptotremateae becomes a synonym of Ocellularieae. As a consequence, the new names S anguinotrema and Sanguinotremateae are introduced to accommodate L . wightii and the tribe including this species and the genus R eimnitzia. Although the studied case is specific to lichen fungi, the approach can be used in a much broader context with any kind of taxon or organism. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179, 436-443. [ABSTRACT FROM AUTHOR]

Jade perch (Scortum barcoo) is a new teleost in the developing aquaculture freshwater finfish grow-out sector in Australia and China. However, key information on the breeding sex determination system (SDS) remains poorly understood, hampering sex control programs and genetic improvement. In this study, the jade perch SDS was examined by investigating genome-wide single-nucleotide polymorphisms (SNPs) using diversity arrays technology and cytogenetics analysis to identify the genomic variants associated with sex-linked regions. Although the cytogenetic results showed no variation in the chromosomal patterns between males and females, one male-specific locus and 13 male-linked loci were observed, suggesting that jade perch exhibits male heterogametic XX/XY SDS. Male-specific loci on the putative Y sex chromosome were also identified as an extremely small proportion of the genome. A homology search of the SNP loci revealed the male-specific loci were homologous to the Gypsy transposable element. This might be a remnant of an initial accumulation of repeats on the Y chromosome at the early stage of sex chromosome differentiation. The results provide a base for sex control breeding biotechnologies and genetic improvements to promote sexual size dimorphism and other new approaches to improve the commercial value of jade perch. • Control of sex and reproduction is a precursor to successful aquaculture. • High-throughput DNA sequencing techniques to investigate sex determination systems. • Initial findings of many sex-linked or sex chromosome-specific molecular markers. • We provide a genetic basis of sexual dimorphism for future manipulation. [ABSTRACT FROM AUTHOR]

Simple Summary: The evolutionary patterns and phylogenetic utility of duplicate control regions (CRs) in 72 individuals of Varanus salvator macromaculatus and other varanids have been observed. Divergence of the two CRs from each individual revealed a pattern of independent evolution in CRs of varanid lineage. This study is a first step towards developing new phylogenetic evolutionary models of the varanid lineage, with accurate evolutionary inferences to provide basic insights into the biology of mitogenomes. Duplicate control regions (CRs) have been observed in the mitochondrial genomes (mitogenomes) of most varanids. Duplicate CRs have evolved in either concerted or independent evolution in vertebrates, but whether an evolutionary pattern exists in varanids remains unknown. Therefore, we conducted this study to analyze the evolutionary patterns and phylogenetic utilities of duplicate CRs in 72 individuals of Varanus salvator macromaculatus and other varanids. Sequence analyses and phylogenetic relationships revealed that divergence between orthologous copies from different individuals was lower than in paralogous copies from the same individual, suggesting an independent evolution of the two CRs. Distinct trees and recombination testing derived from CR1 and CR2 suggested that recombination events occurred between CRs during the evolutionary process. A comparison of substitution saturation showed the potential of CR2 as a phylogenetic marker. By contrast, duplicate CRs of the four examined varanids had similar sequences within species, suggesting typical characteristics of concerted evolution. The results provide a better understanding of the molecular evolutionary processes related to the mitogenomes of the varanid lineage. [ABSTRACT FROM AUTHOR]

Jade perch (Scortum barcoo) is a new teleost in the developing aquaculture freshwater finfish grow-out sector in Australia and China. However, key information on the breeding sex determination system (SDS) remains poorly understood, hampering sex control programs and genetic improvement. In this study, the jade perch SDS was examined by investigating genome-wide single-nucleotide polymorphisms (SNPs) using diversity arrays technology and cytogenetics analysis to identify the genomic variants associated with sex-linked regions. Although the cytogenetic results showed no variation in the chromosomal patterns between males and females, one male-specific locus and 13 male-linked loci were observed, suggesting that jade perch exhibits male heterogametic XX/XY SDS. Male-specific loci on the putative Y sex chromosome were also identified as an extremely small proportion of the genome. A homology search of the SNP loci revealed the male-specific loci were homologous to the Gypsy transposable element. This might be a remnant of an initial accumulation of repeats on the Y chromosome at the early stage of sex chromosome differentiation. The results provide a base for sex control breeding biotechnologies and genetic improvements to promote sexual size dimorphism and other new approaches to improve the commercial value of jade perch. • Control of sex and reproduction is a precursor to successful aquaculture. • High-throughput DNA sequencing techniques to investigate sex determination systems. • Initial findings of many sex-linked or sex chromosome-specific molecular markers. • We provide a genetic basis of sexual dimorphism for future manipulation. [ABSTRACT FROM AUTHOR]

Bighead catfish (Clarias macrocephalus , Günther, 1864) is an important aquacultural species that plays a crucial role in the economy of Southeast Asia. Crossbreeding between female bighead catfish and male African catfish (C. gariepinus , Burchell, 1822) is used to produce hybrids with vigorous phenotypes. However, sterility of the hybrid is a major obstacle to their mass production. There is an emerging hypothesis that the complexity of the sex-determination system between two parental species might affect sterility. Previous studies investigated the co-existence of XX/XY and ZZ/ZW sex-determination systems in the African catfish population in Thailand, but in bighead catfish the sex-determination system remains poorly understood. In this study, the sex-determination system of the bighead catfish was examined using Diversity Arrays Technology to identify the genomic variants associated with sex-linked regions. The results support the hypothesis of the previous study that the bighead catfish might exhibit a male heterogametic XX/XY sex-determination system with multiple male-linked loci. One of the male-linked loci showed homology with the GTSF1L gene, which shows a testis-enriched expression pattern. Two of the male-linked loci were partially homologous to transposable element. Male-linked loci on the putative Y sex chromosome were identified as an extremely small proportion of the genome. A PCR-based DNA marker was developed to validate the male-linked loci in the bighead catfish. Our findings provide novel insights into sex-determination mechanisms in clariid catfish and will contribute to genetic improvements in breeding programs. • The bighead catfish might exhibit a XX/XY sex-determination system. • Putative Y chromosome were identified as an extremely small proportion of the genome. • One of the male-linked loci showed homology with the GTSF1L gene. • GTSF1L is associated with sex determination and plays a role in spermatogenesis. • Our findings contribute to genetic improvements in aquaculture breeding programs. [ABSTRACT FROM AUTHOR]

Sex determination systems (SDSs) in anurans are diverse and have undergone independent evolutionary transitions among species. The mode of sexual reproduction of the rice field frog (Hoplobatrachus rugulosus)—an economically viable, edible amphibian species—is not well known. Previous studies have proposed that threshold temperature conditions may determine sex in these frogs. To elucidate the SDS in H. rugulosus, we karyotyped 10 male and 12 female frogs, and performed fluorescence in situ hybridization combined with sequencing analyses using DArTseq™. Our results revealed a highly conserved karyotype with no sex chromosome heteromorphism, and the sequencing analyses did not identify any consistent sex-linked loci, supporting the hypothesis of temperature-dependent sex determination. The results of this study, and others, on SDSs in the rice field frog and related species also provide support for the theory that heteromorphic sex chromosomes may lead to an evolutionary trap that prevents variable SDSs. These findings add important information to the body of knowledge on H. rugulosus and are likely to have a significant impact on the productivity and economic success of rice field frog farming. [ABSTRACT FROM AUTHOR]

Transposable elements (TEs) are dynamic elements present in all eukaryotic genomes. They can "jump" and amplify within the genome and promote segmental genome rearrangements on both autosomes and sex chromosomes by disruption of gene structures. The Bovine-B long interspersed nuclear element (Bov-B LINE) is among the most abundant TE-retrotransposon families in vertebrates due to horizontal transfer (HT) among vertebrate lineages. Recent studies have shown multiple HTs or the presence of diverse Bov-B LINE groups in the snake lineage. It is hypothesized that Bov-B LINEs are highly dynamic and that the diversity reflects multiple HTs in snake lineages. Partial sequences of Bov-B LINE from 23 snake species were characterized. Phylogenetic analysis resolved at least two Bov-B LINE groups that might correspond to henophidian and caenophidian snakes; however, the tree topology differed from that based on functional nuclear and mitochondrial gene sequences. Several Bov-B LINEs of snakes showed greater than 80% similarity to sequences obtained from insects, whereas the two Bov-B LINE groups as well as sequences from the same snake species classified in different Bov-B LINE groups showed sequence similarities of less than 80%. Calculation of estimated divergence time and pairwise divergence between all individual Bov-B LINE copies suggest invasion times ranging from 79.19 to 98.8 million years ago in snakes. Accumulation of elements in a lineage-specific fashion ranged from 9 × 10−6% to 5.63 × 10−2% per genome. The genomic proportion of Bov-B LINEs varied among snake species but was not directly associated with genome size or invasion time. No differentiation in Bov-B LINE copy number between males and females was observed in any of the snake species examined. Incongruence in tree topology between Bov-B LINEs and other snake phylogenies may reflect past HT events. Sequence divergence of Bov-B LINEs between copies suggests that recent multiple HTs occurred within the same evolutionary timeframe in the snake lineage. The proportion of Bov-B LINEs varies among species, reflecting species specificity in TE invasion. The rapid speciation of snakes, coinciding with Bov-B LINE invasion in snake genomes, leads us to better understand the effect of Bov-B LINEs on snake genome evolution. [ABSTRACT FROM AUTHOR]

To better understand PBI-DdeI satellite DNA located in the centromeric region of python, molecular evolution analysis was conducted on 40 snake species. A ladder-like pattern of DNA bands with repetition of the 194–210 bp monomer was observed in 15 species using PCR. Molecular cloning was performed to obtain 97 AT-rich monomer sequences. Phylogenetic and network analyses showed three PBI-DdeI subfamilies with sequences grouped in species-specific clusters, suggesting rapid evolution. Slow evolution was found in eight species with shared PBI-DdeI sequences, suggesting recent species diversification, allowing PBI-DdeI no time to diverge, with limited homogenization and fixation processes. Quantitative real-time PCR showed large differences in copy number between Python bivittatus and other snakes, consistent with repeat scanning of whole genome sequences. Copy numbers were significantly higher in female Naja kaouthia than in males, concurring with chromosomal distribution of PBI-DdeI specifically localized to female W chromosomes. PBI-DdeI might act as an evolutionary driver with several repeats to promote W chromosome differentiation and heterochromatinization in N. kaouthia. Analysis revealed PBI-DdeI with a reduced copy number, compared to P. bivittatus, in most snakes studied, and it is possible that it subsequently dispersed and amplified on W chromosomes with different functional roles in N. kaouthia. [ABSTRACT FROM AUTHOR]